TABLE 1.
Known pathogenic variants in SLC19A3
| In silico prediction | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Genomic coordinate (GRCh37/hg19) | cDNA (NM_025243.3) | Protein (NP_079519.1) | dbSNP ID | Type of mutation | Polyphen-2 | SIFT | CADD Phred | Allele number | Allele count | Allele frequency | Reference |
| chr2:228,568,440–228,613,489 | – | – | – | Promoter deletion | – | – | – | – | – | – | Flønes et al. (2016) |
| chr2:228567015 | c.20C>A | p.Ser7* | – | Stop-gain | – | – | 35 | – | – | – | Gerards et al. (2013) |
| chr2:228566967 | c.68G>T | p.Gly23Val | rs121917882 | Missense | Probably damaging | Deleterious | 28.1 | 121372 | 1 | 0.0008239% | Kevelam et al. (2013); Pérez-Dueñas et al. (2013); Zeng et al. (2005) |
| chr2:228566960 | c.74dupT | p.Ser26Leufs*19 | – | Frameshift | – | – | 35 | – | – | – | Debs et al. (2010); Sremba, Chang, Elbalalesy, Cambray-Forker, & Abdenur, (2014) |
| chr2:228566953–228566954 | c.81_82dupGA | p.Met28Argfs*2 | – | Frameshift | – | – | 29.6 | 121374 | 2 | 0.001648% | Sremba et al. (2014) |
| chr2:228566905 | c.130A>G | p.Lys44Glu | rs137852957 | Missense | Possibly damaging | Deleterious | 25.5 | – | – | – | Kono et al. (2009); Miyajima and Kono (2010) |
| chr2:228564094 | C.337T>C | p.Tyr113His | rs145999922 | Missense | Probably damaging | Deleterious | 25.5 | 121402 | 7 | 0.005766% | Flønes et al. (2016) |
| chr2:228563967 | c.464C>T | p.Ser155Leu | – | Missense | Probably damaging | Deleterious | 27.3 | – | – | – | Kohrogi et al. (2015) |
| chr2:228563924 | c.507C>G | p.Tyr169* | – | Stop-gain | – | – | 35 | – | – | – | Kevelam et al. (2013) |
| chr2:228563914 | c.517A>G | p.Asn173Asp | – | Missense | Probably damaging | Tolerated | 18.23 | – | – | – | Fassone et al. (2013) |
| chr2:228563904 | c.527C>A | p.Ser176Tyr | – | Missense | Probably damaging | Deleterious | 22.3 | 121400 | 1 | 0.00082% | Kevelam et al. (2013) |
| chr2:228563890 | C.541T>C | p.Ser181Pro | – | Missense | Probably damaging | Tolerated | 22.1 | 121404 | 11 | 0.00906% | Flønes et al. (2016); Kevelam et al. (2013) |
| chr2:228563506–228563536 | c.895_925del31 | p.Val299Profs*11 | – | Frameshift | – | – | 35 | – | – | – | Kevelam et al. (2013) |
| chr2:228563473 | c.958G>C | p.Glu320Gln | – | Missense | Probably damaging | Deleterious | 29.7 | – | – | – | Kono et al. (2009); Miyajima and Kono (2010); Yamada et al. (2010) |
| chr2:228560811 | c.980–14A>G | – | rs200542114 | Exon 4 skipping | – | – | 0.223 | 120582 | 3 | 0.002488% | Debs et al. (2010) |
| chr2:228560795 | c.982delG | p.Ala328Leufs*10 | – | Frameshift | – | – | 35 | – | – | – | Haack et al. (2014) |
| chr2:228560623 | c.1154T>G | p.Leu385Arg | rs563607795 | Missense | Probably damaging | Deleterious | 33 | 121338 | 1 | 0.0008241% | Kevelam et al. (2013) |
| chr2:228552882–228553023 | r.1173_1314del | p.Gln393* | – | Exon 5 deletion | – | – | – | – | – | – | Kevelam et al. (2013) |
| chr2:228553000 | c.1196A>T | p.Asn399Ile | – | Missense | Benign | Deleterious | 24 | – | – | – | Kohrogi et al. (2015) |
| chr2:228552932 | c.1264A>G | p.Thr422Ala | rs121917884 | Missense | Benign | Deleterious | 23.5 | – | – | – | Alfadhel et al. (2013); Distelmaier et al. (2014); Zeng et al. (2005) |
| chr2:228552272 | c.1332C>G | p.Ser444Arg | – | Missense | Possibly damaging | Deleterious | 26.3 | – | – | – | Kevelam et al. (2013) |